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- PDB-8tgc: Structure of Red beta C-terminal domain in complex with SSB C-ter... -

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Basic information

Entry
Database: PDB / ID: 8tgc
TitleStructure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 4
Components
  • Plasmid-derived single-stranded DNA-binding protein
  • Recombination protein bet
KeywordsDNA BINDING PROTEIN / Recombination / Recombineering / Single Strand Annealing / Single-stranded DNA binding protein / genome engineering
Function / homology
Function and homology information


nucleoid / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / DNA binding
Similarity search - Function
Bacteriophage lambda, Recombination protein bet / RecT family / RecT family / Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Recombination protein bet / Plasmid-derived single-stranded DNA-binding protein
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.484 Å
AuthorsBell, C.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-2212951 United States
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Structural Basis for the Interaction of Red beta Single-Strand Annealing Protein with Escherichia coli Single-Stranded DNA-Binding Protein.
Authors: Zakharova, K. / Liu, M. / Greenwald, J.R. / Caldwell, B.C. / Qi, Z. / Wysocki, V.H. / Bell, C.E.
History
DepositionJul 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Recombination protein bet
A: Recombination protein bet
C: Plasmid-derived single-stranded DNA-binding protein
D: Plasmid-derived single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)21,4584
Polymers21,4584
Non-polymers00
Water3,747208
1
B: Recombination protein bet
D: Plasmid-derived single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)10,7292
Polymers10,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-11 kcal/mol
Surface area5510 Å2
MethodPISA
2
A: Recombination protein bet
C: Plasmid-derived single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)10,7292
Polymers10,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-9 kcal/mol
Surface area5340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.596, 67.895, 71.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Recombination protein bet


Mass: 9428.625 Da / Num. of mol.: 2 / Mutation: N-TERMINAL GSHM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: bet, betA, red-beta, redB / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: P03698
#2: Protein/peptide Plasmid-derived single-stranded DNA-binding protein / SSB / Helix-destabilizing protein


Mass: 1300.392 Da / Num. of mol.: 2 / Fragment: C-terminal peptide / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P28044
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.4 M ammonium phosphate dibasic, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2020 / Details: KB mirrors, fixed focus
RadiationMonochromator: Kohzu HLD-15 Double Crystal cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.484→35.66 Å / Num. obs: 19557 / % possible obs: 63.3 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.033 / Rrim(I) all: 0.082 / Net I/σ(I): 13.4
Reflection shellResolution: 1.484→1.643 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 978 / CC1/2: 0.554 / Rpim(I) all: 0.475 / Rrim(I) all: 0.853 / % possible all: 12.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
autoPROC1.1.7data reduction
Aimless0.7.4data scaling
MOLREP11.4.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.484→35.66 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.233 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.121 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2589 953 4.873 %
Rwork0.2029 18604 -
all0.206 --
obs-19557 63.289 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.724 Å2
Baniso -1Baniso -2Baniso -3
1-0.117 Å2-0 Å20 Å2
2---0.065 Å20 Å2
3----0.053 Å2
Refinement stepCycle: LAST / Resolution: 1.484→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 0 208 1466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121276
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161218
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.6311731
X-RAY DIFFRACTIONr_angle_other_deg0.4921.5892808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.645155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.38755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69410227
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.9311062
X-RAY DIFFRACTIONr_chiral_restr0.0640.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021486
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02266
X-RAY DIFFRACTIONr_nbd_refined0.2230.2270
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.21100
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2632
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2694
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2133
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2870.210
X-RAY DIFFRACTIONr_nbd_other0.1570.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.28
X-RAY DIFFRACTIONr_mcbond_it2.2332.185632
X-RAY DIFFRACTIONr_mcbond_other2.2282.184632
X-RAY DIFFRACTIONr_mcangle_it3.4393.886783
X-RAY DIFFRACTIONr_mcangle_other3.4393.887784
X-RAY DIFFRACTIONr_scbond_it3.6212.707644
X-RAY DIFFRACTIONr_scbond_other3.6192.706645
X-RAY DIFFRACTIONr_scangle_it5.8494.787948
X-RAY DIFFRACTIONr_scangle_other5.8464.786949
X-RAY DIFFRACTIONr_lrange_it7.80125.8581513
X-RAY DIFFRACTIONr_lrange_other7.63724.9441460
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.484-1.5230.29530.409480.40122510.9830.9252.26570.395
1.523-1.5640.273100.3761620.3721840.8710.9357.87550.368
1.564-1.610.39150.3443530.34621310.9180.93617.26890.339
1.61-1.6590.356270.3015720.30420590.9390.9529.09180.289
1.659-1.7130.36600.2739240.27820210.9410.95448.68880.259
1.713-1.7730.274610.25511920.25619280.9540.95764.98960.229
1.773-1.840.239880.22613610.22718870.9580.96576.78860.194
1.84-1.9150.323770.25512880.25918200.9430.958750.203
1.915-20.374510.30512500.30817440.9120.93674.59860.229
2-2.0970.401530.24712880.25316730.8950.95380.15540.203
2.097-2.210.258730.22215110.22415920.9450.96999.49750.199
2.21-2.3440.362650.27613010.28115180.9110.94389.98680.218
2.344-2.5050.211770.18313450.18514260.9730.97999.71950.173
2.505-2.7050.237510.18510520.18713220.9620.97983.43420.179
2.705-2.9610.238450.1911860.19112330.9560.97799.83780.192
2.961-3.3080.293580.18810500.19311140.9470.97899.46140.2
3.308-3.8140.17430.1578990.15810120.9820.98593.0830.174
3.814-4.6580.263350.1447770.1488630.9670.98794.09040.171
4.658-6.5320.207370.1936490.1946890.9810.98199.56460.228
6.532-35.660.222240.1923960.1934250.9770.97698.82350.249

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